mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
3aacd46da2
* backfilled modules with meta.yml that had no license identifier * harmonized BSD license names * whitespace linting at modules/unzip/meta.yml:12 * harmonized software from US NIH-NCBI/NIST to 'US-Government-Work' * Update modules/bcftools/index/meta.yml `bcftools` is dual-licensed, use associative array to allow for multiple licenses Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Michael L Heuer <heuermh@acm.org>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: gatk4_applybqsr
|
|
description: Apply base quality score recalibration (BQSR) to a bam file
|
|
keywords:
|
|
- bqsr
|
|
- bam
|
|
tools:
|
|
- gatk4:
|
|
description: |
|
|
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
|
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
|
and high-performance computing features make it capable of taking on projects of any size.
|
|
homepage: https://gatk.broadinstitute.org/hc/en-us
|
|
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
|
|
doi: 10.1158/1538-7445.AM2017-3590
|
|
licence: ['Apache-2.0']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: BAM file from alignment
|
|
pattern: "*.{bam}"
|
|
- bqsr_table:
|
|
type: file
|
|
description: Recalibration table from gatk4_baserecalibrator
|
|
- fasta:
|
|
type: file
|
|
description: The reference fasta file
|
|
- fastaidx:
|
|
type: file
|
|
description: Index of reference fasta file
|
|
- dict:
|
|
type: file
|
|
description: GATK sequence dictionary
|
|
- intervalsBed:
|
|
type: file
|
|
description: Bed file with the genomic regions included in the library (optional)
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- bam:
|
|
type: file
|
|
description: Recalibrated BAM file
|
|
pattern: "*.{bam}"
|
|
|
|
authors:
|
|
- "@yocra3"
|